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High-quality reads were selected using Newbler sequence filtering at default settings.
CNVs were called based on 980 million high-quality reads (Map Q≥ 10, Supplementary Data 12) on average for each sample.
Total reads represent the number of high-quality reads.
After filtering, 87,598,529 high-quality reads remained.
Using high-quality reads is expected to identify true variants.
We obtained high-quality reads for 743 clones.
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After filtering, 70,453,120 high quality reads were obtained and used for de novo assembly (Table 1).
The remaining high quality reads were checked for the existence of chimeric sequences.
As additional quality criteria we used only variants with a coverage >10× of high quality reads.
They were regarded as high quality reads.
Thus filtered, high quality reads were used for further analysis.
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